Biocurious is a weblog about biology, quantified.

Semi-digital lab notebooks

by PhilipJ on 18 January 2009

Going on a year ago, I talked a bit about digital lab notebooks and their use as a potential replacement for the paper notebooks we all carry around. The idea of a digital notebook is very appealing: searchable, easily archived, portable (if you wanted to place it on the internet), etc. The downsides, however, are also obvious: having a computer next to you on the bench to write is not always ideal, since spilling a solvent on paper causes relatively little harm compared to frying the electronics of a laptop. It is also much slower to do a quick sketch on a computer than on a piece of paper.

When I first tried to “go digital”, I set up a wiki on my group’s server and would try to include information in it as I was going about my day. I found it, unfortunately, quite cumbersome. When the kinds of things you are doing at the optical table are alignment, position readings, power measurements, etc, I found it crucial to keep my paper notebook with me to quickly record these numbers and make sketches of the optical elements, and I was loathe to transcribe this information into the wiki later, mostly because scanning or redrawing the figures digitally takes too long.

When it comes to data analysis, however, everything has to be done on a computer, as it is just not feasible to plot thousands of data points by hand in a paper notebook. My computer algebra system of choice is Mathematica, and because of Mathematica’s notebook system, it became extremely straightforward to include sufficient commentary among the analysis and calculations. The important “working” details of my day are recorded on paper that is heavy on scribbles, numbers, and comments on the minutiae of a particular instrument or measurement, followed by references to specific data files collected that day. The Mathematica notebooks where I visualize and analyze data are then filled with the relevant comments about the data collection and subsequent analysis, but not usually the random scribbles that you need to keep on paper while leading-up to and actually taking a measurement. Having everything organized by date makes it simple to correlate between paper and digital notebooks.

All this is to say that I’ve found a happy medium between analog and digital data retention. The paper notebooks will remain as a permanent record of the day-to-day activities in the laboratory, while digital notebooks are used to flesh out important collected data. The only downside is that Mathematica is not an open platform, but as long as there are free Notebook readers available, I’ll try not to get too worried.



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